Variant report

Variant	rs4574378
Chromosome Location	chr4:74402790-74402791
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10004505	0.88[EUR][1000 genomes]
rs10011536	0.80[AMR][1000 genomes]
rs10016403	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10019146	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs10028196	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10028276	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10029673	0.89[CEU][hapmap]
rs10212657	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10213305	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10518115	0.81[CEU][hapmap]
rs10805065	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10938077	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10938078	0.94[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10938079	0.89[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10938085	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10938086	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10938088	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1159624	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11728915	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11729144	0.81[AMR][1000 genomes]
rs11733262	0.89[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11935001	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11939341	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11943798	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1247668	0.90[CEU][hapmap]
rs1247670	0.81[CEU][hapmap]
rs1247671	0.81[CEU][hapmap]
rs12503916	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs12504448	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12507775	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs12508661	0.81[CEU][hapmap]
rs12508974	0.87[EUR][1000 genomes]
rs12510629	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13103378	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13115877	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13120998	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13124940	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13135124	0.81[AMR][1000 genomes]
rs13144296	0.90[CEU][hapmap]
rs13149172	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13150405	0.86[ASN][1000 genomes]
rs13353732	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1358592	0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1528917	0.90[CEU][hapmap]
rs1528918	0.87[CEU][hapmap]
rs1528924	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1569204	0.90[CEU][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1590115	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1590116	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16849461	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs16849508	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs16849628	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs16849677	0.90[CEU][hapmap]
rs16849727	1.00[CEU][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17192413	0.81[CEU][hapmap]
rs1881611	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1894293	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1919469	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919479	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1997332	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1997333	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2008288	0.90[CEU][hapmap]
rs2040354	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2071097	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2141465	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2141470	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2178290	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2178292	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204736	0.90[ASN][1000 genomes]
rs28838047	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34238679	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34468776	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35233345	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35988516	0.90[ASN][1000 genomes]
rs4235119	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4267703	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4267704	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4267705	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4438732	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4618279	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4631010	0.91[ASN][1000 genomes]
rs4694173	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56011127	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56384466	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62312137	0.81[AMR][1000 genomes]
rs6446937	0.94[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446938	0.94[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446939	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446941	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6837506	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6852149	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6852772	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs72647083	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7676460	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7682201	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs997478	0.81[AMR][1000 genomes]
rs9990707	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9997572	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9999939	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3430875	chr4:74243646-74420354	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4574378	MUC7	cis	cerebellum	SCAN
rs4574378	ART3	cis	cerebellum	SCAN
rs4574378	CXCL2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74399600-74403400	Enhancers	Fetal Intestine Large	intestine
2	chr4:74400000-74405400	Strong transcription	Liver	Liver
3	chr4:74401800-74402800	Enhancers	Hela-S3	cervix
4	chr4:74402200-74402800	Enhancers	GM12878-XiMat	blood

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